Comparing work done on RNA seq data
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4.7 years ago
bioinfo456 ▴ 150

Hi all,

I'm trying to put together a paper. Is there any ways of comparing my work done with the following paper :-

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182507#sec027

I have used sample pairs to extract differentially expressed genes and obtained approx 5k genes. Whereas in the above mentioned paper the concept of extracting differentially expressed genes is completely different. Is there any ways of comparing work done by me against the work done in this paper?

Please help.

RNA-Seq differential expression analysis deseq2 • 1.2k views
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Your question is far too vague to answer. What is the purpose of your paper? How is what you might be proposing in your paper relevant to the paper you cite? What is the subject of your paper?

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  1. Classification of cancer subtype (renal cell).

My approach for the purpose is entirely different but I use the same tool (deseq2) and one of the 4 datasets used in paper I’ve mentioned above.

My question here is, should I even compare the work done or write it in an independent manner?

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Renal cell cancer is majorly divided into 3 classes (ie; KICH KIRP KIRC). I used deseq2 to identify DEG for each class. Suppose x was the resulting subset of genes for KICH similarly y and z for KIRP and KIRC, I eliminated all intersections for each class (ie; s = (x u y u z) - ((x n y n z) u (x n y) u (y n z) u (z n x))). As a result of which I got approx 5k genes. Now, I have a 1000 samples out of which I’ve divided 700 for training and 300 for testing. I’ve extracted s genes out of the training set and trained a classifier model. I’ve obtained a certain significant results.

I’m trying to put together a paper. There exists a paper which makes use of deseq2 and also the same data set. Now my question is how do I go about writing this paper? Their methodology is completely different. They have used DEGs as low as 250 genes and obtained a certain result which is comparatively less than what I got. Please share your thoughts. Thanks.

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Will biostars be first author?

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Will biostars show up at the conference? If yes then yes they will be. That would be dope.

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Check this article about RNA-seq analysis tool comparison. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190152

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